Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA

Degradation-driven vegetation-soil-microbe interactions alter microbial carbon use efficiency in Moso bamboo forests

Microbial carbon utilization efficiency (CUE) is a crucial indicator for evaluating the efficiency of soil carbon sequestration and transformation, which is applied to quantify the proportion of soil carbon extracted by microbes for anabolism (growth) and catabolism (respiration). Previous studies have shown that the degradation of Moso bamboo forests (Phyllostachys edulis) destroyed the aboveground bamboo structure, reduced vegetation carbon storage, and weakened ecosystem carbon sequestration capacity. Interestingly, soil organic carbon stocks are gradually increasing. However, the mechanism by which degradation-induced changes in soil and vegetation characteristics affect microbial CUE and drive soil carbon sequestration remains unclear. Here we selected four stands with the same origin but different degradation years (intensive management, CK; 2 years' degradation, DM1; 6 years' degradation, DM2; and 10 years' degradation, DM3) based on the local management profiles. The principle of space-for-time substitution was used to investigate the changes in microbial CUE along a degradation time and to further identify the controlling biotic and abiotic factors. Our finding showed that microbial CUE increased by 12.27 %, 31.01 %, and 55.95 %, respectively, compared with CK; whereas microbial biomass turnover time decreased from 23.99 ± 1.11 to 17.16 ± 1.20 days. Promoting microbial growth was the main pathway to enhance microbial CUE. Massive inputs of vegetative carbon replenished soil carbon substrate content, and altered microbial communities and life history strategy, which in turn promoted microbial growth and increased microbial CUE. These findings provide theoretical support for the interactions between carbon dynamics and microbial physiology in degraded bamboo forests, and reinforce the importance of vegetation and microbial properties and soil carbon substrates in predicting microbial CUE.

Land-use intensification exerts a greater influence on soil microbial communities than seasonal variations in the Taihu Lake region, China

The Taihu Lake region has undergone intensive land-use conversions from natural wetlands (NW) to conventional rice-wheat rotation fields (RW) and further to greenhouse vegetable fields (GH). Nevertheless, the effects of these conversions on soil microbes, particularly in wetland ecosystem, are not well explicit. To explore the impact of land-use intensification on soil microbial communities, monthly soil samples were obtained from replicate plots representing three land-use types (NW, RW, and GH) in subtropical wetlands and then subjected to amplicon sequencing. Land-use intensification had direct effects on bacterial and fungal community composition, with a more pronounced impact on bacteria than on fungi. These changes in bacterial communities were closely correlated with variations in soil environmental variables, such as NO3--N, pH, and electrical conductivity. Land-use intensification led to a decrease in bacterial deterministic processes, with an opposing trend observed in the fungal community. In addition, arable lands (RW and GH), which are affected by anthropogenic activities, exhibited more complex networks. Potential metabolic functional groups in GH had higher absolute abundance. Seasonal variations significantly influenced microbial diversity, composition, and potential metabolic functional groups within each land-use type, particularly in summer, although the magnitude of this impact was much smaller than the impact of land-use intensification. Our findings emphasize the importance of comprehending the ecological consequences of land-use intensification in wetlands for sustainable resource management and biodiversity conservation.

Profiling the fecal microbiome and its modulators across the lifespan in the Netherlands

Defining what constitutes a healthy microbiome throughout our lives remains an ongoing challenge. Understanding to what extent host and environmental factors can influence it has been the primary motivation for large population studies worldwide. Here, we describe the fecal microbiome of 3,746 individuals (0-87 years of age) in a nationwide study in the Netherlands, in association with extensive questionnaires. We validate previous findings, such as infant-adult trajectories, and explore the collective impact of our variables, which explain over 40% of the variation in microbiome composition. We identify associations with less explored factors, particularly those ethnic related, which show the largest impact on the adult microbiome composition, diversity, metabolic profiles, and CAZy (carbohydrate-active enzyme) repertoires. Understanding the sources of microbiome variability is crucial, given its potential as a modifiable target with therapeutic possibilities. With this work, we aim to serve as a foundational element for the design of health interventions and fundamental research.

Genome-resolved metagenomics reveals the nitrifiers enrichment and species succession in activated sludge under extremely low dissolved oxygen

Nitrification, a process carried out by aerobic microorganisms that oxidizes ammonia to nitrate via nitrite, is an indispensable step in wastewater nitrogen removal. To facilitate energy and carbon savings, applying low dissolved oxygen (DO) is suggested to shortcut the conventional biological nitrogen removal pathway, however, the impact of low DO on nitrifying communities within activated sludge is not fully understood. This study used genome-resolved metagenomics to compare nitrifying communities under extremely low- and high-DO. Two bioreactors were parallelly operated to perform nitrification and DO was respectively provided by limited gas-liquid mass transfer from the atmosphere (AN reactor, DO < 0.1 mg/L) and by sufficient aeration (AE reactor, DO > 5.0 mg/L). Low DO was thought to limit nitrifiers growth; however, we demonstrated that complete nitrification could still be achieved under the extremely low-DO conditions, but with no nitrite accumulation observed. Kinetic analysis showed that after long-term exposure to low DO, nitrifiers had a higher oxygen affinity constant and could maintain a relatively high nitrification rate, particularly at low levels of DO (<0.2 mg/L). Community-level gene analysis indicated that low DO promoted enrichment of nitrifiers (the genera Nitrosomonas and Nitrospira, increased by 2.3- to 4.3-fold), and also harbored with 2.3 to 5.3 times higher of nitrification functional genes. Moreover, 46 high-quality (>90 % completeness and <5 % contamination) with 3 most abundant medium-quality metagenome-assembled genomes (MAGs) were retrieved using binning methods. Genome-level phylogenetic analysis revealed the species succession within nitrifying populations. Surprisingly, compared to DO-rich conditions, low-DO conditions were found to efficiently suppressed the ordinary heterotrophic microorganisms (e.g., the families Anaerolineales, Phycisphaerales, and Chitinophagales), but selected for the specific candidate denitrifiers (within phylum Bacteroidota). This study provides new microbial insights to demonstrate that low-DO favors the enrichment of autotrophic nitrifiers over heterotrophs with species-level successions, which would facilitate the optimization of energy and carbon management in wastewater treatment.

Metagenome reveals the midgut microbial community of Haemaphysalis qinghaiensis ticks collected from yaks and Tibetan sheep

BACKGROUND

Haemaphysalis qinghaiensis is a tick species distributed only in China. Due to its ability to transmit a variety of pathogens, including species of the genera Anaplasma, Rickettsia, Babesia, and Theileria, it seriously endangers livestock husbandry. However, the microbial community of the midgut of H. qinghaiensis females collected from yaks and Tibetan sheep has not yet been characterized using metagenomic sequencing technology.

METHODS

Haemaphysalis qinghaiensis were collected from the skins of yaks and Tibetan sheep in Gansu Province, China. Genomic DNA was extracted from the midguts and midgut contents of fully engorged H. qinghaiensis females collected from the two hosts. Metagenomic sequencing technology was used to analyze the microbial community of the two groups.

RESULTS

Fifty-seven phyla, 483 genera, and 755 species were identified in the two groups of samples. The ticks from the two hosts harbored common and unique microorganisms. At the phylum level, the dominant common phyla were Proteobacteria, Firmicutes, and Mucoromycota. At the genus level, the dominant common genera were Anaplasma, Ehrlichia, and Pseudomonas. At the species level, bacteria including Anaplasma phagocytophilum, Ehrlichia minasensis, and Pseudomonas aeruginosa along with eukaryotes such as Synchytrium endobioticum and Rhizophagus irregularis, and viruses such as the orf virus, Alphadintovirus mayetiola, and Parasteatoda house spider adintovirus were detected in both groups. In addition, the midgut of H. qinghaiensis collected from yaks had unique microbial taxa including two phyla, eight genera, and 23 species. Unique microorganisms in the midgut of H. qinghaiensis collected from Tibetan sheep included two phyla, 14 genera, and 32 species. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the functional genes of the microbiome of H. qinghaiensis were annotated to six pathways, and the metabolic pathways included 11 metabolic processes, in which the genes involved in carbohydrate metabolism were the most abundant, followed by the genes involved in lipid metabolism.

CONCLUSIONS

These findings indicate that most of the microbial species in the collected H. qinghaiensis ticks were the same in both hosts, but there were also slight differences. The analytical data from this study have enhanced our understanding of the midgut microbial composition of H. qinghaiensis collected from different hosts. The database of H. qinghaiensis microbe constructed from this study will lay the foundation for predicting tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding vector competency and interactions with ticks and midgut microorganisms.

Biogeochemical stability of organic covers and mine wastes under climate change simulated mesocosms

Mine environments in boreal and sub-boreal zones are expected to experience extreme weather events, increases in temperature, and shifts in precipitation patterns. Climate change impacts on geochemical stability of tailings contaminants and reclamation structures have been identified as important climate-related challenges to Canadian mining sector. Adapting current reclamation strategies for climate change will improve long-term efficiency and viability of mine tailings remediation/restoration strategies under a changing climate. Accordingly, mesocosm experiments were conducted to investigate associations of climate-driven shifts in microbial communities and functions with changes in the geochemistry of organic covers and underlying tailings. Our results show that warming appears to significantly reduce C:N of organic cover and promote infiltration of nitrogen into deeper, unoxidized strata of underlying tailings. We also observed an increase in the abundance of some nitrate reducers and sulfide oxidizers in microbial communities in underlying tailings. These results raise the concern that warming might trigger oxidation of sulfide minerals (linked to nitrate reduction) in deeper unoxidized strata where the oxygen has been eliminated. Therefore, it would be necessary to have monitoring programs to track functionality of covers in response to climate change conditions. These findings have implications for development of climate resilient mine tailings remediation/restoration strategies.

Microbial core communities in activated sludge plants are strongly affected by immigration and geography

BACKGROUND

The microbiota in wastewater treatment plants (WWTPs) and incoming wastewater is critical for the treatment process, the preservation of natural ecosystems and human health, and for the recovery of resources and achievement of sustainability goals. Both core species and conditionally rare and abundant taxa (CRAT) are considered process-critical but little is known about identity as well as true functional and ecological importance. Here, we present a comprehensive investigation of the microbiota of 84 municipal activated sludge (AS) plants with nutrient removal treating ~ 70% of all wastewater within a confined geographical area, Denmark (43,000 km2). With the use of an ecosystem-specific database (MiDAS 5.2), species-level classification allowed us to investigate the core and CRAT species, whether they were active, and important factors determining their presence.

RESULTS

We established a comprehensive catalog of species with names or placeholder names showing each plant contained approx. 2,500 different species. Core and CRAT represented in total 258 species, constituting around 50% of all reads in every plant. However, not all core and CRAT could be regarded as process-critical as growth rate calculations revealed that 43% did not grow in the AS plants and were present only because of continuous immigration from the influent. Analyses of regional microbiota differences and distance decay patterns revealed a stronger effect for species than genera, demonstrating that geography had a clear effect on the AS microbiota, even across a limited geographical area such as Denmark (43,000 km2).

CONCLUSIONS

The study is the first comprehensive investigation of WWTPs in a confined geographical area providing new insights in our understanding of activated sludge microbiology by introducing a concept of combining immigration and growth calculation with identifying core and CRAT to reveal the true ecosystem-critical organisms. Additionally, the clear biogeographical pattern on this scale highlights the need for more region-level studies to find regional process-critical taxa (core and CRAT), especially at species and amplicon sequence variant (ASV) level.

Residual disinfectant effectively suppresses Legionella species in drinking water distribution systems supplied by surface water in Minnesota, USA

Seven public water systems in Minnesota, USA were analyzed from one to five times over a two-year period to assess temporal changes in the concentrations of total bacteria, Legionella spp., and Legionella pneumophila from source (i.e., raw water) through the water treatment process to the end water user. Bacterial biomass was collected by filtering large volumes of raw water (12 to 425 L, median: 38 L) or finished and tap water (27 to 1205 L, median: 448 L) using ultrafiltration membrane modules. Quantitative PCR (qPCR) was then used to enumerate all bacteria (16S rRNA gene fragments), all Legionella spp. (ssrA), and Legionella pneumophila (mip). Total coliforms, Escherichia coli, and L. pneumophila also were quantified in the water samples via cultivation. Median concentrations of total bacteria and Legionella spp. (ssrA) in raw water (8.5 and 4.3 log copies/L, respectively) decreased by about 2 log units during water treatment. The concentration of Legionella spp. (ssrA) in water collected from distribution systems inversely correlated with the total chlorine concentration for chloraminated systems significantly (p = 0.03). Although only 8 samples were collected from drinking water distribution systems using free chlorine as a residual disinfectant, these samples had significantly lower concentrations of Legionella spp. (ssrA) than samples collected from the chloraminated systems (p = 5 × 10-4). There was considerable incongruity between the results obtained via cultivation-independent (qPCR) and cultivation-dependent assays. Numerous samples were positive for L. pneumophila via cultivation, none of which tested positive for L. pneumophilia (mip) via qPCR. Conversely, a single sample tested positive for L. pneumophilia (mip) via qPCR, but this sample tested negative for L. pneumophilia via cultivation. Overall, the results suggest that conventional treatment is effective at reducing, but not eliminating, Legionella spp. from surface water supplies and that residual disinfection is effective at suppressing these organisms within drinking water distribution systems.

Effect of a Bacillus velezensis and Lysinibacillus fusiformis-based biofertilizer on phosphorus acquisition and grain yield of soybean

Introduction

Phosphate-solubilizing bacteria that function through acidification (organic acid synthesis) or mineralization (production of enzymes such as phytase and phosphatases) have been explored as a biotechnological alternative to enhance plant access to phosphorus (P) retained in organic and inorganic forms in agricultural soils. This study tested the hypothesis that applying a biofertilizer composed of a recognized phosphate-solubilizing bacterium (Bacillus velezensis - endophytic strain BVPS01) and an underexplored plant growth-promoting bacterium (Lysinibacillus fusiformis - endophytic strain BVPS02) would improve the growth and grain yield of Glycine max L. plants.

Methods

Initial in vitro tests assessed the functional traits of these bacteria, and a mix of strains BVPS01 and BVPS02 was produced and tested under field conditions to evaluate its agronomic efficiency.

Results

The results confirmed the hypothesis that the tested biofertilizer enhances the agronomic performance of G. max plants in the field. The B. velezensis strain (BVPS01) was found to be more effective than the L. fusiformis strain (BVPS02) in solubilizing phosphates via the phosphatase enzyme production pathway, indicated by the expression of the phoC and phoD genes. In contrast, L. fusiformis was more effective in solubilizing phosphates through organic acid and phytase-related pathways, in addition to synthesizing indole-3-acetic acid and increasing the mitotic index in the root meristem of G. max plants. These strains exhibited biological compatibility, and the formulated product based on these rhizobacteria enhanced root development and increased the number of nodules and flowers, positively affecting 1000-grain weight, grain yield, and grain P content.

Discussion

Thus, the tested biofertilizer demonstrated potential to improve root growth and increase both the yield and quality of soybean crops, making it a sustainable and low-cost strategy.

Long-read sequencing reveals two chromosomes and one plasmid in Vibrio sp. strain MAO6 isolated from a Marine Beach in Fukui, Japan

A marine bacterium Vibrio sp. strain MAO6 was isolated from a marine beach in Fukui, Japan. Its complete genome comprises two circular chromosomes (3,418,677 bp and 1,629,627 bp) and one circular plasmid (299,686 bp).

Soil pH amendment alters the abundance, diversity, and composition of microbial communities in two contrasting agricultural soils

Soil microorganisms are the most active participants in terrestrial ecosystems, and have key roles in biogeochemical cycles and ecosystem functions. Despite the extensive research on soil pH as a key predictor of microbial community and composition, a limitation of these studies lies in determining whether bacterial and/or fungal communities are directly or indirectly influenced by pH. We conducted a controlled laboratory experiment to investigate the effects of soil pH amendment (+/- 1-2 units) with six levels on soil microbial communities in two contrasting Chinese agricultural soils (pH 8.43 in Dezhou, located in the North China Plain, Shandong vs pH 6.17 in Wuxi, located in the Taihu Lake region, Jiangsu, east China). Results showed that the fungal diversity and composition were related to soil pH, but the effects were much lower than the effects of soil pH on bacterial community in two soils. The diversity and composition of bacterial communities were more closely associated with soil pH in Wuxi soils compared to Dezhou soils. The alpha diversity of bacterial communities peaked near in situ pH levels in both soils, displaying a quadratic fitting pattern. Redundancy analysis and variation partition analysis indicated that soil pH affected bacterial community and composition by directly imposing a physiological constraint on soil bacteria and indirectly altering soil characteristics (e.g., nutrient availability). The study also examined complete curves of taxa relative abundances at the phylum and family levels in response to soil pH, with most relationships conforming to a quadratic fitting pattern, indicating soil pH is a reliable predictor. Furthermore, soil pH amendment affected the transformation of nitrogen and the abundances of functional genes involved in the nitrogen cycle, and methane production and consumption. Overall, results from this study would enhance our comprehension of how soil microorganisms in contrasting farmlands will respond to soil pH changes, and would contribute to more effective soil management and conservation strategies.

IMPORTANCE

This study delves into the impact of soil pH on microbial communities, investigating whether pH directly or indirectly influences bacterial and fungal communities. The research involved two contrasting soils subjected to a 1-2 pH unit amendment. Results indicate bacterial community composition was shaped by soil pH through physiological constraints and nutrient limitations. We found that most taxa relative abundances at the phylum and family levels responded to pH with a quadratic fitting pattern, indicating that soil pH is a reliable predictor. Additionally, soil pH was found to significantly influence the predicted abundance of functional genes involved in the nitrogen cycle as well as in methane production and consumption processes. These insights can contribute to develop more effective soil management and conservation strategies.

Two-year Monitoring of Microbiological Water Quality in Small Water Supply Systems: Implications for Microbial Risk Management

Small water supply systems (SWSSs) are often more vulnerable to waterborne disease outbreaks. In Japan, many SWSSs operate without regulation under the Waterworks Law, yet there is limited investigation into microbial contamination and the associated health risks. In this study, the microbiological water quality of four SWSSs that utilize mountain streams as water sources and do not install water treatment facilities were monitored for over 2 years. In investigated SWSSs, the mean heterotrophic plate counts were below 350 CFU/mL, and the total bacterial loads (16S rDNA concentration) ranged from 4.71 to 5.35 log10 copies/mL. The results also showed the consistent presence of fecal indicator bacteria (FIB), i.e., Escherichia coli and Clostridium perfringens, suggesting the potential of fecal pollution. E. coli was then utilized as an indicator to assess the health risk posed by E. coli O157:H7 and Campylobacter jejuni. The results indicated that the estimated mean annual risk of infection and disability-adjusted life years (DALYs) exceeded acceptable levels in all SWSSs for the two reference pathogens. To ensure microbial water safety, implementing appropriate water treatment facilities with an estimated mean required reduction of 5-6 log10 was necessary. This study highlighted the potential microbial contamination and health risk level in SWSSs that utilize mountain streams as water sources, even though the water sources were almost not affected by human activities. Furthermore, this study would also be helpful in supporting risk-based water management to ensure a safe water supply in SWSSs.

Comammox Nitrospira among dominant ammonia oxidizers within aquarium biofilter microbial communities

Nitrification by aquarium biofilters transforms ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Prior to the discovery of complete ammonia-oxidizing ("comammox" or CMX) Nitrospira, previous research revealed that ammonia-oxidizing archaea (AOA) dominated over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Here, we profiled aquarium biofilter microbial communities and quantified the abundance of all three known ammonia oxidizers using 16S rRNA gene sequencing and quantitative PCR (qPCR), respectively. Biofilter and water samples were each collected from representative residential and commercial freshwater and saltwater aquaria. Distinct biofilter microbial communities were associated with freshwater and saltwater biofilters. Comammox Nitrospira amoA genes were detected in all 38 freshwater biofilter samples (average CMX amoA genes: 2.2 × 103 ± 1.5 × 103 copies/ng) and dominant in 30, whereas AOA were present in 35 freshwater biofilter samples (average AOA amoA genes: 1.1 × 103 ± 2.7 × 103 copies/ng) and only dominant in 7 of them. The AOB were at relatively low abundance within biofilters (average of 3.2 × 101 ± 1.1 × 102 copies of AOB amoA genes/ng of DNA), except for the aquarium with the highest ammonia concentration. For saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. Additional sequencing of Nitrospira amoA genes revealed differential distributions, suggesting niche adaptation based on water chemistry (e.g., ammonia, carbonate hardness, and alkalinity). Network analysis of freshwater microbial communities demonstrated positive correlations between nitrifiers and heterotrophs, suggesting metabolic and ecological interactions within biofilters. These results demonstrate that comammox Nitrospira plays a previously overlooked, but important role in home aquarium biofilter nitrification.

IMPORTANCE

Nitrification is a crucial process that converts toxic ammonia waste into less harmful nitrate that occurs in aquarium biofilters. Prior research found that ammonia-oxidizing archaea (AOA) were dominant over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Our study profiled microbial communities of aquarium biofilters and quantified the abundance of all currently known groups of aerobic ammonia oxidizers. The findings reveal that complete ammonia-oxidizing (comammox) Nitrospira were present in all freshwater aquarium biofilter samples in high abundance, challenging our previous understanding of aquarium nitrification. We also highlight niche adaptation of ammonia oxidizers based on salinity. The network analysis of freshwater biofilter microbial communities revealed significant positive correlations among nitrifiers and other community members, suggesting intricate interactions within biofilter communities. Overall, this study expands our understanding of nitrification in aquarium biofilters, emphasizes the role of comammox Nitrospira, and highlights the value of aquaria as microcosms for studying nitrifier ecology.

Status of Cassava Witches' Broom Disease in the Philippines and Identification of Potential Pathogens by Metagenomic Analysis

Cassava witches' broom disease (CWBD) is one of the most devastating diseases of cassava (Manihot esculenta Crantz), and it threatens global production of the crop. In 2017, a phytoplasma, Candidatus Phytoplasma luffae (Ca. P. luffae), was reported in the Philippines, and it has been considered as the causal agent, despite unknown etiology and transmission of CWBD. In this study, the nationwide occurrence of CWBD was assessed, and detection of CWBD's pathogen was attempted using polymerase chain reaction (PCR) and next-generation sequencing (NGS) techniques. The results showed that CWBD has spread and become severe, exhibiting symptoms such as small leaf proliferation, shortened internodes, and vascular necrosis. PCR analysis revealed a low phytoplasma detection rate, possibly due to low titer, uneven distribution, or absence in the CWBD-symptomatic cassava. In addition, NGS techniques confirm the PCR results, revealing the absence or extremely low phytoplasma read counts, but a surprisingly high abundance of fastidious and xylem-limited fungus, Ceratobasidium sp. in CWBD-symptomatic plants. These findings cast doubt over the involvement of phytoplasma in CWBD and instead highlight the potential association of Ceratobasidium sp., strongly supporting the recent findings in mainland Southeast Asia. Further investigations are needed to verify the etiology of CWBD and identify infection mechanisms of Ceratobasidium sp. to develop effective diagnostic and control methods for disease management.

Changes in sediment greenhouse gases production dynamics in an estuarine wetland following invasion by Spartina alterniflora

Invasive Spartina alterniflora (S. alterniflora) has significant impacts on sediment biogeochemical cycling in the tidal wetlands of estuaries and coasts. However, the impact of exotic Spartina alterniflora invasion on greenhouse gases (GHGs) production dynamics in sediments remain limited. Here, we investigated the dynamics of sediment physicochemical properties, GHGs production rates, and microbial gene abundances in a native Cyperus malacensis habitat and three invasive S. alterniflora habitats (6-, 10-, and 14-year) in the Minjiang River Estuary, China. The methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) production rates varied both spatially and seasonally, while microbial gene abundances (bacterial and fungal gene abundances) and organic matter (TOC and TN) only varied spatially. GHGs production rates were also characterized by higher values in surface sediment (0-10 cm) compared to subsurface sediment (10-20 cm) and by seasonal variations with higher values in summer than in winter. S. alterniflora invasion can significantly increase CH4 and CO2 production rates, organic matter, and microbial gene abundances (p < 0.05). Temperature, organic matter and microbial gene abundances were the most dominating factor controlling the spatio-temporal variations of CH4 and CO2 production rates. Overall, our findings highlighted the significant role of S. alterniflora invasion in regulating GHGs production rates in coastal wetland sediments and provided fundamental data for estimating GHGs emissions and carbon sequestration in the complex tidal wetlands.

Characterisation of microbial communities and quantification of antibiotic resistance genes in Italian wastewater treatment plants using 16S rRNA sequencing and digital PCR

The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in humans, animals and environment is a growing threat to public health. Wastewater treatment plants (WWTPs) are crucial in mitigating the risk of environmental contamination by effectively removing contaminants before discharge. However, the persistence of ARB and ARGs even after treatment is a challenge for the management of water system. To comprehensively assess antimicrobial resistance dynamics, we conducted a one-year monitoring study in three WWTPs in central Italy, both influents and effluents. We used seasonal sampling to analyze microbial communities by 16S rRNA, as well as to determine the prevalence and behaviour of major ARGs (sul1, tetA, blaTEM, blaOXA-48, blaCTX-M-1 group, blaKPC) and the class 1 Integron (int1). Predominant genera included in order: Arcobacter, Acinetobacter, Flavobacterium, Pseudarcobacter, Bacteroides, Aeromonas, Trichococcus, Cloacibacterium, Pseudomonas and Streptococcus. A higher diversity of bacterial communities was observed in the effluents compared to the influents. Within these communities, we also identified bacteria that may be associated with antibiotic resistance and pose a significant threat to human health. The mean concentrations (in gene copies per liter, gc/L) of ARGs and int1 in untreated wastewater (absolute abundance) were as follows: sul1 (4.1 × 109), tetA (5.2 × 108), blaTEM (1.1 × 108), blaOXA-48 (2.1 × 107), blaCTX-M-1 group (1.1 × 107), blaKPC (9.4 × 105), and int1 (5.5 × 109). The mean values in treated effluents showed reductions ranging from one to three log. However, after normalizing to the 16S rRNA gene (relative abundance), it was observed that in 37.5 % (42/112) of measurements, the relative abundance of ARGs increased in effluents compared to influents. Furthermore, correlations were identified between ARGs and bacterial genera including priority pathogens. This study improves our understanding of the dynamics of ARGs and provides insights to develop more effective strategies to reduce their spread, protecting public health and preserving the future efficacy of antibiotics.

Ammonium oxidation from concentrated synthetic wastewater and landfill leachate using partial nitritation in sequencing batch reactor

Partial nitritation (PN) is a novel treatment for nitrogen removal using aerobic ammonium oxidation with reduced oxygen requirements compared to conventional nitrification. This study evaluated the performance of the PN process and the factors influencing nitrogen removal from landfill leachate. During the reactivation of biomass, the results showed 70% ammonium removal, but only 20% total nitrogen removal. Further analysis showed that low nitrite accumulation and high nitrate production promoted the growth of nitrite-oxidizing bacteria (NOB). The ammonium removal activity after soaking the cultivated biomass in synthetic water and leachate was measured to be 0.57, 0.1, 0.17, and 0.25 g N•g VSS-1•d-1 for synthetic wastewater and leachate soaking for synthetic wastewater, 12 h, 3 days, and 7 days, respectively. The study found abundant ammonium-oxidizing bacteria (AOB) and NOBs in biomass soaked in synthetic wastewater. However, soaking in leachate promoted AOB growth and inhibited NOB growth making leachate suitable for PN. PRACTITIONER POINTS: The study found that with a longer leachate-soaking period for biomass, ammonium removal activity increases, which in turn increases ammonium conversions during the PN process. Ammonium-oxidizing bacteria (AOB) can acclimate to landfill leachate substrate and grow with a longer soaking period. Nitrite-oxidizing bacteria (NOB) were inhibited by landfill leachate substrate, which is beneficial for nitrite accumulation. Anabolized DO can convert nitrite to nitrate rapidly, which results in higher nitrate accumulation compared to nitrite accumulation. Hence, the DO level has to be sufficiently low to prevent nitrite oxidation and nitrate accumulation.

Effect of photostimulation through red LED light radiation on natural fermentation of table olives: An innovative case study with Negrinha the Freixo variety

In this study, for the first time, red LED light radiation was applied to the fermentation process of table olives using the Negrinha de Freixo variety. Photostimulation using LED light emission (630 ± 10 nm) is proposed to shorten and speed up this stage and reduce time to market. Several physical-chemical characteristics and microorganisms (total microbial count of mesophilic aerobic, molds, yeasts, and lactic acid bacteria) and their sequence during fermentation were monitored. The fermentation occurred for 122 days, with two irradiation periods for red LED light. The nutritional composition and sensory analysis were performed at the end of the process. Fermentation under red LED light increased the viable yeast and lactic acid bacteria (LAB) cell counts and decreased the total phenolics in olives. Even though significant differences were observed in some color parameters, the hue values were of the same order of magnitude and similar for both samples. Furthermore, the red LED light did not play a relevant change in the texture profile, preventing the softening of the fruit pulp. Similarly, LED light did not modify the existing type of microflora but increased species abundance, resulting in desirable properties and activities. The species identified were yeasts - Candida boidinii, Pichia membranifaciens, and Saccharomyces cerevisiae, and bacteria - Lactobacillus plantarum and Leuconostoc mesenteroides, being the fermentative process dominated by S. cerevisiae and L. plantarum. At the end of fermentation (122 days), the irradiated olives showed less bitterness and acidity, higher hardness, and lower negative sensory attributes than non-irradiated. Thus, the results of this study indicate that red LED light application can be an innovative technology for table olives production.

Comparative analysis of microbiome inhabiting oxygenated and deoxygenated habitats using V3 and V6 metabarcoding of 16S rRNA gene

We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.

CopG1, a Novel Transcriptional Regulator Affecting Symbiosis in Bradyrhizobium sp. SUTN9-2

The symbiotic interaction between leguminous and Bradyrhizobium sp. SUTN9-2 mainly relies on the nodulation process through Nod factors (NFs), while the type IV secretion system (T4SS) acts as an alternative pathway in this symbiosis. Two copies of T4SS (T4SS1 and T4SS2) are located on the chromosome of SUTN9-2. ΔT4SS1 reduces both nodule number and nitrogenase activity in all SUTN9-2 nodulating legumes. The functions of three selected genes (copG1, traG1, and virD21) within the region of T4SS1 were examined. We generated deleted mutants and tested them in Vigna radiata cv. SUT4. ΔtraG1 and ΔvirD21 exhibited lower invasion efficiency at the early stages of root infection but could be recently restored. In contrast, ΔcopG1 completely hindered nodule organogenesis and nitrogenase activity in all tested legumes. ΔcopG1 showed low expression of the nodulation gene and ttsI but exhibited high expression levels of the T4SS genes, traG1 and trbE1. The secreted proteins from ΔT4SS1 were down-regulated compared to the wild-type. Although ΔcopG1 secreted several proteins after flavonoid induction, T3SS (nopP and nopX) and the C4-dicarboxylate transporter (dct) were not detected. These results confirm the crucial role of the copG1 gene as a novel key regulator in the symbiotic relationship between SUTN9-2 and legumes.

Evaluating the antibacterial efficacy of a silver nanocomposite surface coating against nosocomial pathogens as an antibiofilm strategy to prevent hospital infections

Antimicrobial nanocoatings may be a means of preventing nosocomial infections, which account for significant morbidity and mortality. The role of hospital sink traps in these infections is also increasingly appreciated. We describe the preparation, material characterization and antibacterial activity of a pipe cement-based silver nanocoating applied to unplasticized polyvinyl chloride, a material widely used in wastewater plumbing. Three-dimensional surface topography imaging and scanning electron microscopy showed increased roughness in all surface finishes versus control, with grinding producing the roughest surfaces. Silver stability within nanocoatings was >99.89% in deionized water and bacteriological media seeded with bacteria. The nanocoating exhibited potent antibiofilm (99.82-100% inhibition) and antiplanktonic (99.59-99.99% killing) activity against three representative bacterial species and a microbial community recovered from hospital sink traps. Hospital sink trap microbiota were characterized by sequencing the 16S rRNA gene, revealing the presence of opportunistic pathogens from genera including Pseudomonas, Enterobacter and Clostridioides. In a benchtop model sink trap system, nanocoating antibiofilm activity against this community remained significant after 11 days but waned following 25 days. Silver nanocoated disks in real-world sink traps in two university buildings had a limited antibiofilm effect, even though in vitro experiments using microbial communities recovered from the same traps demonstrated that the nanocoating was effective, reducing biofilm formation by >99.6% and killing >98% of planktonic bacteria. We propose that conditioning films forming in the complex conditions of real-world sink traps negatively impact nanocoating performance, which may have wider relevance to development of antimicrobial nanocoatings that are not tested in the real-world.

Nitrous oxide respiration in acidophilic methanotrophs

Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.

Soil microbial community fragmentation reveals indirect effects of fungicide exposure mediated by biotic interactions between microorganisms

Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.

The gut-brain-axis: A positive relationship between gut microbial dysbiosis and glioblastoma brain tumour

The glioblastoma brain tumour (GBM) stands out as the most aggressive and resistant-to-treatment malignancy. Nevertheless, the gut-brain connection plays a pivotal role in influencing the growth and activation of the central nervous system. In this particular investigation, we aimed to assess and characterize the gut microbial ecosystem in GBM patients, both quantitatively and qualitatively. We collected faecal samples from 15 healthy volunteers and 25 GBM patients. To delve into the microbial content, we employed PCR-DGGE, targeting the V3 region of the 16S rRNA gene, and conducted qPCR to measure the levels of crucial intestinal bacteria. For a more in-depth analysis, high-throughput sequencing was performed on a selection of 20 random faecal samples (10 from healthy individuals and 10 from GBM patients), targeting the V3+V4 region of the 16S rRNA gene. Our findings from examining the richness and diversity of the gut microbiota unveiled that GBM patients exhibited significantly higher microbial diversity compared to healthy individuals. At the phylum level, Proteobacteria saw a significant increase, while Firmicutes experienced a noteworthy decrease in the GBM group. Moving down to the family level, we observed significantly elevated levels of Enterobacteriaceae, Bacteroidaceae, and Lachnospiraceae in GBM patients, while levels of Veillonellaceae, Rikenellaceae, and Prevotellaceae were notably lower. Delving into genera statistics, we noted a substantial increase in the abundance of Parasutterella, Escherichia-Shigella, and Bacteroides, alongside significantly lower levels of Ruminococcus 2, Faecalibacterium, and Prevotella_9 in the GBM group compared to the control group. Furthermore, when examining specific species, we found a significant increase in Bacteroides vulgatus and Escherichia coli in the GBM group. These observations collectively indicate a marked dysbiosis in the gut microbial composition of GBM patients. Additionally, the GBM group exhibited notably higher levels of alpha diversity when compared to the control group. This increase in diversity suggests a significant bacterial overgrowth in the gut of GBM patients in contrast to the controls. As a result, this research opens up potential avenues to gain a better understanding of the underlying mechanisms, pathways, and potential treatments for GBM, stemming from the significant implications of gut microbial dysbiosis in these patients.

Patient-derived pathogenic microbe deposition enhances exposure risk in pediatric clinics

Healthcare-associated infections (HAIs) pose significant risks to pediatric patients in outpatient settings. To prevent HAIs, understanding the sources and transmission routes of pathogenic microorganisms is crucial. This study aimed to identify the sources of opportunistic bacterial pathogens (OBPs) in pediatric outpatient settings and determine their transmission routes. Furthermore, assessing the public health risks associated with the core OBPs is important. We collected 310 samples from various sites in pediatric outpatient areas and quantified the bacteria using qPCR and CFU counting. We also performed 16S rRNA gene and single-bacterial whole-genome sequencing to profile the transmission routes and antibiotic resistance characteristics of OBPs. We observed significant variations in microbial diversity and composition among sampling sites in pediatric outpatient settings, with active communication of the microbiota between linked areas. We found that the primary source of OBPs in multi-person contact areas was the hand surface, particularly in pediatric patients. Five core OBPs, Staphylococcus epidermidis, Acinetobacter baumannii, Pseudomonas aeruginosa, Streptococcus mitis, and Streptococcus oralis, were mainly derived from pediatric patients and spread into the environment. These OBPs accumulated at multi-person contact sites, resulting in high microbial diversity in these areas. Transmission tests confirmed the challenging spread of these pathogens, with S. epidermidis transferring from the patient's hand to the environment, leading to an increased abundance and emergence of related strains. More importantly, S. epidermidis isolated from pediatric patients carried more antibiotic-resistance genes. In addition, two strains of multidrug-resistant A. baumannii were isolated from both a child and a parent, confirming the transmission of the five core OBPs centered around pediatric patients and multi-person contact areas. Our results demonstrate that pediatric patients serve as a significant source of OBPs in pediatric outpatient settings. OBPs carried by pediatric patients pose a high public health risk. To effectively control HAIs, increasing hand hygiene measures in pediatric patients and enhancing the frequency of disinfection in multi-person contact areas remains crucial. By targeting these preventive measures, the spread of OBPs can be reduced, thereby mitigating the risk of HAIs in pediatric outpatient settings.

Effect of the cleaning and disinfection methods on the hygienic conditions of fermentation tanks of table olives (Olea europaea L.) Negrinha de Freixo cultivar

This study aimed to evaluate and identify the microbial community attached to the surfaces of fermenter tanks used in table olive Negrinha de Freixo cultivar processing through molecular analysis and verify if the cleaning/disinfection was done correctly. Four fermentation tanks previously used in table olive processing were sampled at three different inside areas: upper, middle, and lower. Before sampling, four cleaning/disinfection methods were applied to the tanks, including (i) pressurised water; (ii) a disinfectant product used to clean bowls (Vasiloxe); (iii) 10% sodium hydroxide solution (caustic soda liquid); and (iv) a disinfectant product used by the wine industry (Hosbit). For each sample collected, mesophilic aerobic bacteria, yeast and moulds (YMC), lactic acid bacteria (LAB), as well as total coliforms (TC) and Pseudomonas aeruginosa were evaluated. The results showed significant differences between the different cleaning/disinfection methods applied. The fermenter sanitised with only pressurised water showed a greater abundance of microorganisms than the others. Mesophilic aerobic bacteria were the predominant population, with counts ranging between 2.63 and 5.56 log10 CFU/100 cm2, followed by the moulds (3.11-5.03 log10 CFU/100 cm2) and yeasts (2.42-5.12 log10 CFU/100 cm2). High diversity of microbial communities was observed between the different fermenter tanks. The most abundant species belonged to Aureobasidium, Bacillaceae, Cladosporium, and Rhodotorula genera. LAB, TC, and P. aeruginosa were not detected. This study hopes to improve hygienic conditions and increase the quality assurance and safety of the final product.

Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress

The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.

Mitigating methane emissions and global warming potential while increasing rice yield using biochar derived from leftover rice straw in a tropical paddy soil

The sustainable management of leftover rice straw through biochar production to mitigate CH4 emissions and enhance rice yield remains uncertain and undefined. Therefore, we evaluated the effects of using biochar derived from rice straw left on fields after harvest on greenhouse gas emissions, global warming potential (GWP), and rice yield in the paddy field. The experiment included three treatments: chemical fertilizer (CF), rice straw (RS, 10 t ha-1) + CF, and rice straw-derived biochar (BC, 3 t ha-1 based on the amount of product remaining after pyrolysis) + CF. Compared with CF, BC + CF significantly reduced cumulative CH4 and CO2 emissions, net GWP, and greenhouse gas emission intensity by 42.9%, 37.4%, 39.5%, and 67.8%, respectively. In contrast, RS + CF significantly increased cumulative CH4 emissions and net GWP by 119.3% and 13.8%, respectively. The reduced CH4 emissions were mainly caused by the addition of BC + CF, which did not increase the levels of dissolved organic carbon and microbial biomass carbon, consequently resulting in reduced archaeal abundance, unlike those observed in RS + CF. The BC + CF also enhanced soil total organic carbon content and rice grain yield. This study indicated that using biochar derived from leftover rice straw mitigates greenhouse gas emissions and improves rice productivity in tropical paddy soil.

Bacterial Community Structure Responds to Soil Management in the Rhizosphere of Vine Grape Vineyards

The microbial communities of the rhizospheres of vineyards have been subject to a considerable body of research, but it is still unclear how the applied soil cultivation methods are able to change the structure, composition, and level of diversity of their communities. Rhizosphere samples were collected from three neighbouring vineyards with the same time of planting and planting material (rootstock: Teleki 5C; Vitis vinifera: Müller Thurgau). Our objective was to examine the diversity occurring in bacterial community structures in vineyards that differ only in the methods of tillage procedure applied, namely intensive (INT), extensive (EXT), and abandoned (AB). For that we took samples from two depths (10-30 cm (shallow = S) and 30-50 cm (deep = D) of the grape rhizosphere in each vineyard and the laboratory and immediately prepared the slices of the roots for DNA-based analysis of the bacterial communities. Bacterial community structure was assessed by means of PCR-DGGE analysis carried out on the v3 region of 16S rRNA gene. Based on the band composition of the DGGE profiles thus obtained, the diversity of the microbial communities was evaluated and determined by the Shannon-Weaver index (H'). Between the AB and EXT vineyards at the S depth, the similarity of the community structure was 55%; however, the similarity of the D samples was more than 80%, while the difference between the INT samples and the other two was also higher than 80%. Based on our results, we can conclude that intensive cultivation strongly affects the structure and diversity of the bacterial community.

Bacterial diversity in agricultural drainage ditches shifts with increasing urea-N concentrations

Urea-based fertilizers applied to crop fields can enter the surface waters of adjacent agricultural drainage ditches and contribute to the nitrogen (N) loading in nearby watersheds. Management practices applied in drainage ditches promote N removal by the bacterial communities, but little is known about the impacts of excess urea fertilizer from crop fields on the bacterial diversity in these ditches. In 2017, sediments from drainage ditches next to corn and soybean fields were sampled to determine if fertilizer application and high urea-N concentrations alters bacterial diversity and urease gene abundances. A mesocosm experiment was paired with a field study to determine which bacterial groups respond to high urea-N concentrations. The bacterial diversity in the ditch next to corn fields was significantly different from the other site. The bacterial orders of Rhizobiales, Bacteroidales, Acidobacteriales, Burkholderiales, and Anaerolineales were most abundant in the ditch next to corn and increased after the addition of urea-N (0.5 mg N L-1) during the mesocosm experiment. The results of our study suggests that urea-N concentrations >0.07 mg N L-1, which are higher than concentrations associated with downstream harmful algal blooms, can lead to shifts in the bacterial communities of agricultural drainage ditches.

Isolation of mucosa-associated microbiota dysbiosis in the ascending colon in hepatitis C virus post-sustained virologic response cirrhotic patients

Background

Achieving sustained virologic response (SVR) in patients infected with hepatitis C virus (HCV) reduces all-cause mortality. However, the mechanisms and risk factors for liver fibrosis and portal hypertension post-SVR remain incompletely understood. In the gut-liver axis, mucosa-associated microbiota (MAM) substantially influence immune and metabolic functions, displaying spatial heterogeneity at the anatomical intestinal site. We analyzed MAM composition and function to isolate the locoregional MAM involved in chronic liver disease progression in HCV post-SVR patients.

Methods

We collected MAM samples from three intestinal sites (terminal ileum, ascending colon, and sigmoid colon) via brushing during colonoscopy in 23 HCV post-SVR patients and 25 individuals without liver disease (controls). The 16S rRNA of bacterial DNA in specimens collected with a brush and in feces was sequenced. The molecular expression of intestinal tissues and hepatic tissues were evaluated by quantitative real-time PCR.

Results

In the post-SVR group, the microbial β-diversity of MAM, especially in the ascending colon, differed from the control group and was associated with liver fibrosis progression. In PICRUSt analysis, MAM in the ascending colon in the liver cirrhosis (LC) group showed compromised functions associated with the intestinal barrier and bile acid production, and FGF19 expression was markedly decreased in the terminal ileum biopsy tissue in the LC group. At the genus level, six short-chain fatty acid (SCFA)-producing bacterial genera, Blautia, Alistipes, Roseburia, Agathobaculum, Dorea, and Pseudoflavonifractor were reduced in the ascending colon of post-SVR LC patients.

Conclusion

In patients of HCV post-SVR, we identified the association between the degree of liver fibrosis and dysbiosis of mucosa-associated SCFA-producing bacterial genera that may be related to intestinal barrier and bile acid production in the ascending colon.

Occurrence of sulfate-reducing bacteria in well water: identification of anaerobic sulfidogenic bacterial enrichment cultures

Bacteriological studies of well water mainly focus on aerobic and facultative aerobic coliform bacteria. However, the presence of obligate anaerobic bacteria in well water, especially sulfate-reducing bacteria (SRB), possible causative agents of some diseases, is often ignored. In this study, the presence of SRB and coexisting anaerobic bacteria with SRB in sulfate-reducing enrichment cultures obtained from 10 well water samples in Istanbul was investigated. A nested polymerase chain reaction-denaturing gradient gel electrophoresis strategy was performed to characterize the bacterial community structure of the enrichments. The most probable number method was used to determine SRB number. Out of 10, SRB growth was observed in only one (10%) enrichment culture and the SRB number was low (<10 cells/mL). Community members were identified as Desulfolutivibrio sulfodismutans and Anaerosinus sp. The results show that SRB coexist with Anaerosinus sp., and this may indicate poor water quality, posing a risk to public health. Furthermore, Anaerosinus sp., found in the human intestinal tract, may be used as an alternative anaerobic fecal indicator. It is worth noting that the detection of bacteria using molecular analyzes following enrichment culture techniques can bring new perspectives to determine the possible origin and presence of alternative microbial indicators in aquatic environments.

Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis

Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.

Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.

Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water

As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.

Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly

BACKGROUND

Microbial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil colonization to determine the role of bacterial interactions in soil community assembly. We hypothesized that experimentally manipulating the physical distance between bacterial cells will modify the interaction strengths leading to differences in microbial community composition, with increasing distance between neighbors favoring poor competitors.

RESULTS

We found significant differences in both bacterial community diversity, composition and co-occurrence networks after soil colonization that were related to physical distancing. We show that reducing distances between cells resulted in a loss of bacterial diversity, with at least 41% of the dominant OTUs being significantly affected by physical distancing. Our results suggest that physical distancing may differentially modulate competitiveness between neighboring species depending on the taxa present in the community. The mixing of communities that assembled at high and low cell densities did not reveal any "home field advantage" during coalescence. This confirms that the observed differences in competitiveness were due to biotic rather than abiotic filtering.

CONCLUSIONS

Our study demonstrates that the competitiveness of bacteria strongly depends on cell density and community membership, therefore highlighting the fundamental role of microbial interactions in the assembly of soil communities.

Maribacter halichondriae sp. nov., isolated from the marine sponge Halichondria panicea, displays features of a sponge-associated life style

A new member of the family Flavobacteriaceae (termed Hal144T) was isolated from the marine breadcrumb sponge Halichondria panicea. Sponge material was collected in 2018 at Schilksee which is located in the Kiel Fjord (Baltic Sea, Germany). Phylogenetic analysis of the full-length Hal144T 16S rRNA gene sequence revealed similarities from 94.3 to 96.6% to the nearest type strains of the genus Maribacter. The phylogenetic tree of the 16S rRNA gene sequences depicted a cluster of strain Hal144T with its closest relatives Maribacter aestuarii GY20T (96.6%) and Maribacter thermophilus HT7-2T (96.3%). Genome phylogeny showed that Maribacter halichondriae Hal144T branched from a cluster consisting of Maribacter arenosus, Maribacter luteus, and Maribacter polysiphoniae. Genome comparisons of strain Maribacter halichondriae Hal144T with Maribacter sp. type strains exhibited average nucleotide identities in the range of 75-76% and digital DNA-DNA hybridisation values in the range of 13.1-13.4%. Compared to the next related type strains, strain Hal144T revealed unique genomic features such as phosphoenolpyruvate-dependent phosphotransferase system pathway, serine-glyoxylate cycle, lipid A 3-O-deacylase, 3-hexulose-6-phosphate synthase, enrichment of pseudogenes and of genes involved in cell wall and envelope biogenesis, indicating an adaptation to the host. Strain Hal144T was determined to be Gram-negative, mesophilic, strictly aerobic, flexirubin positive, resistant to aminoglycoside antibiotics, and able to utilize N-acetyl-β-D-glucosamine. Optimal growth occurred at 25-30 °C, within a salinity range of 2-6% sea salt, and a pH range between 5 and 8. The major fatty acids identified were C17:0 3-OH, iso-C15:0, and iso-C15:1 G. The DNA G + C content of strain Hal144T was 41.4 mol%. Based on the polyphasic approach, strain Hal144T represents a novel species of the genus Maribacter, and we propose the name Maribacter halichondriae sp. nov. The type strain is Hal144T (= DSM 114563T = LMG 32744T).

An Aminoglycoside-Sparing Regimen with Double Beta-Lactam to Successfully Treat Granulicatella adiacens Prosthetic Aortic Valve Endocarditis-Time to Change Paradigm?

(1) Background: Granulicatella adiacens is a former nutritionally variant streptococci (NVS). NVS infective endocarditis (IE) is generally characterized by a higher rate of morbidity and mortality, partially due to difficulties in choosing the most adequate microbiological culture method and the most effective treatment strategy, and partially due to higher rates of complications, such as heart failure, peripheral septic embolism, and peri-valvular abscess, as well as a higher rate of valve replacement. Depending on the affected valve (native valve endocarditisNVE, or prosthetic valve endocarditisPVE), the American Heart Association (AHA) 2015 treatment guidelines (GLs) suggest penicillin G, ampicillin, or ceftriaxone plus gentamicin (2 weeks for NVE and up to 6 weeks for PVE), while vancomycin alone may be a reasonable alternative in patients who are intolerant of β-lactam therapy. The European Society of Cardiology (ESC) 2023 GLs recommend treating NVE with penicillin G, ceftriaxone, or vancomycin for 6 weeks, suggesting combined with an aminoglycoside (AG) for at least the first 2 weeks only for PVE; likewise, the same recommendations for IE due to Enterococcus faecalis. (2) Methods: Starting from the case of a 51-year-old man with G. adiacens aortic bio-prosthesis IE who was successfully treated with aortic valve replacement combined with double beta-lactams, an AG-sparing regimen, we performed microbiology tests in order to validate this potential treatment change. (3) Results: As for E. faecalis IE, we found that the combination of ampicillin plus cephalosporines (like ceftriaxone or ceftobiprole) showed a synergistic effect in vitro, probably due to wider binding to penicillin-binding proteins (PBPs), thus contributing to enhanced bacterial killing and good clinical outcome, as well as avoiding the risk of nephrotoxicity due to AG association therapy. (4) Conclusions: Further studies are required to confirm this hypothesis, but double beta-lactams and an adequate sourcecontrol could be a choice in treating G. adiacens IE.

Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability

Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well-understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early, and late growing season. Phospholipid fatty acid (PLFA) and quantitative PCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota, and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.

Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils

Microbial arsenic transformations play essential roles in controlling pollution and ameliorating risk. This study combined high-throughput sequencing and PCR-based approaches targeting both the 16 S rRNA and arsenic functional genes to investigate the temporal and spatial dynamics of the soil microbiomes impacted by high arsenic contamination (9.13 to 911.88 mg/kg) and to investigate the diversity and abundance of arsenic functional genes in soils influenced by an arsenic gradient. The results showed that the soil microbiomes were relatively consistent and mainly composed of Actinobacteria (uncultured Gaiellales and an unknown_67 - 14 bacterium), Proteobacteria, Firmicutes (particularly, Bacillus), Chloroflexi, and Acidobacteria (unknown_Subgroup_6). Although a range of arsenic functional genes (e.g., arsM, arsC, arrA, and aioA) were identified by shotgun metagenomics, only the arsM gene was detected by the PCR-based method. The relative abundance of the arsM gene accounted for 0.20%-1.57% of the total microbial abundance. Combining all analyses, arsenic methylation mediated by the arsM gene was proposed to be a key process involved in the arsenic biogeochemical cycle and mitigation of arsenic toxicity. This study advances our knowledge about arsenic mechanisms over the long-term in highly contaminated soils.

Supplementation with Astragalus Root Powder Promotes Rumen Microbiota Density and Metabolome Interactions in Lambs

The gut microbiota is highly symbiotic with the host, and the microbiota and its metabolites are essential for regulating host health and physiological functions. Astragalus, as a feed additive, can improve animal immunity. However, the effects of Astragalus root powder on the rumen microbiota and their metabolites in lambs are not apparent. In this study, thirty healthy Hu sheep lambs with similar body weights (17.42 ± 2.02 kg) were randomly selected for the feeding experiment. Lambs were fed diets supplemented with 0.3% Astragalus root powder, and the rumen microbiota density and metabolome were measured to determine the effects of Astragalus on the health of lambs in the rumen. The results showed that the relative abundance of Butyrivibrio fibrisolvens (Bf), Ruminococcus flavefaciens (Rf), Succiniclasticum (Su), and Prevotella (Pr) in the rumen was increased in the Astragalus group (p < 0.01), and metabolic profiling showed that the metabolites, such as L-lyrosine and L-leucine, were upregulated in the Astragalus group (p < 0.01). KEGG functional annotation revealed that upregulated metabolites were mainly enriched in the pathways of amino acid metabolism, lipid metabolism, fatty acid biosynthesis, and bile secretion in the Astragalus group, and downregulated metabolites were enriched in the pathways of methane metabolism and other pathways. Correlation analysis revealed that butyric acid was positively correlated with Roseburia and Blautia (p < 0.05) and negatively correlated with Desulfovibrio (p < 0.05). Thus, by analyzing the interactions of Astragalus root powder with the density of rumen microorganisms and their metabolites in lambs, it was shown that Astragalus root powder could improve the structure of rumen microbiota and their metabolites and then participate in the regulation of amino acid metabolism, lipid metabolism, immune metabolism, and other pathways to improve the efficiency of energy absorption of the lambs.

Impact of dry density and incomplete saturation on microbial growth in bentonite clay for nuclear waste storage

AIMS

Many countries are in the process of designing a deep geological repository (DGR) for long-term storage of used nuclear fuel. For several designs, used fuel containers will be placed belowground, with emplacement tunnels being backfilled using a combination of highly compacted powdered bentonite clay buffer boxes surrounded by a granulated "gapfill" bentonite. To limit the potential for microbiologically influenced corrosion of used fuel containers, identifying conditions that suppress microbial growth is critical for sustainable DGR design. This study investigated microbial communities in powdered and gapfill bentonite clay incubated in oxic pressure vessels at dry densities between 1.1 g cm-3 (i.e. below repository target) and 1.6 g cm-3 (i.e. at or above repository target) as a 1-year time series.

RESULTS

Our results showed an initial (i.e. 1 month) increase in the abundance of culturable heterotrophs associated with all dry densities <1.6 g cm-3, which reveals growth during transient low-pressure conditions associated with the bentonite saturation process. Following saturation, culturable heterotroph abundances decreased to those of starting material by the 6-month time point for all 1.4 and 1.6 g cm-3 pressure vessels, and the most probable numbers of culturable sulfate-reducing bacteria (SRB) remained constant for all vessels and time points. The 16S rRNA gene sequencing results showed a change in microbial community composition from the starting material to the 1-month time point, after which time most samples were dominated by sequences associated with Pseudomonas, Bacillus, Cupriavidus, and Streptomyces. Similar taxa were identified as dominant members of the culture-based community composition, demonstrating that the dominant members of the clay microbial communities are viable. Members of the spore-forming Desulfosporosinus genus were the dominant SRB for both clay and culture profiles.

CONCLUSIONS

After initial microbial growth while bentonite was below target pressure in the early phases of saturation, microbial growth in pressure vessels with dry densities of at least 1.4 g cm-3 was eventually suppressed as bentonite neared saturation.

Contrary effects of increasing temperatures on the spread of antimicrobial resistance in river biofilms

River microbial communities regularly act as the first barrier of defense against the spread of antimicrobial resistance genes (ARGs) that enter environmental microbiomes through wastewater. However, how the invasion dynamics of wastewater-borne ARGs into river biofilm communities will shift due to climate change with increasing average and peak temperatures remains unknown. Here, we aimed to elucidate the effects of increasing temperatures on the naturally occurring river biofilm resistome, as well as the invasion success of foreign ARGs entering through wastewater. Natural biofilms were grown in a low-anthropogenic impact river and transferred to artificial laboratory recirculation flume systems operated at three different temperatures (20°C, 25°C, and 30°C). After 1 week of temperature acclimatization, significant increases in the abundance of the naturally occurring ARGs in biofilms were detected at higher temperatures. After this acclimatization period, biofilms were exposed to a single pulse of wastewater, and the invasion dynamics of wastewater-borne ARGs were analyzed over 2 weeks. After 1 day, wastewater-borne ARGs were able to invade the biofilms successfully with no observable effect of temperature on their relative abundance. However, thereafter, ARGs were lost at a far increased rate at 30°C, with ARG levels dropping to the initial natural levels after 14 days. Contrary to the lower temperatures, ARGs were either lost at slower rates or even able to establish themselves in biofilms with stable relative abundances above natural levels. Hence, higher temperatures come with contrary effects on river biofilm resistomes: naturally occurring ARGs increase in abundance, while foreign, invading ARGs are lost at elevated speeds.IMPORTANCEInfections with bacteria that gained resistance to antibiotics are taking millions of lives annually, with the death toll predicted to increase. River microbial communities act as a first defense barrier against the spread of antimicrobial resistance genes (ARGs) that enter the environment through wastewater after enrichment in human and animal microbiomes. The global increase in temperature due to climate change might disrupt this barrier effect by altering microbial community structure and functions. We consequently explored how increasing temperatures alter ARG spread in river microbial communities. At higher temperatures, naturally occurring ARGs increased in relative abundance. However, this coincided with a decreased success rate of invading foreign ARGs from wastewater to establish themselves in the communities. Therefore, to predict the effects of climate change on ARG spread in river microbiomes, it is imperative to consider if the river ecosystem and its resistome are dominated by naturally occurring or invading foreign ARGs.

Phenotypic, molecular, and in silico characterization of coumarin as carbapenemase inhibitor to fight carbapenem-resistant Klebsiella pneumoniae

BACKGROUND

Carbapenems represent the first line treatment of serious infections caused by drug-resistant Klebsiella pneumoniae. Carbapenem-resistant K. pneumoniae (CRKP) is one of the urgent threats to human health worldwide. The current study aims to evaluate the carbapenemase inhibitory potential of coumarin and to test its ability to restore meropenem activity against CRKP. Disk diffusion method was used to test the antimicrobial susceptibility of K. pneumoniae clinical isolates to various antibiotics. Carbapenemase genes (NDM-1, VIM-2, and OXA-9) were detected using PCR. The effect of sub-MIC of coumarin on CRKP isolates was performed using combined disk assay, enzyme inhibition assay, and checkerboard assay. In addition, qRT-PCR was used to estimate the coumarin effect on expression of carbapenemase genes. Molecular docking was used to confirm the interaction between coumarin and binding sites within three carbapenemases.

RESULTS

K. pneumoniae clinical isolates were found to be multi-drug resistant and showed high resistance to meropenem. All bacterial isolates harbor at least one carbapenemase-encoding gene. Coumarin significantly inhibited carbapenemases in the crude periplasmic extract of CRKP. The checkerboard assay indicated that coumarin-meropenem combination was synergistic exhibiting a fractional inhibitory concentration index ≤ 0.5. In addition, qRT-PCR results revealed that coumarin significantly decreased carbapenemase-genes expression. Molecular docking revealed that the binding energies of coumarin to NDM1, VIM-2, OXA-48 and OXA-9 showed a free binding energy of -7.8757, -7.1532, -6.2064 and - 7.4331 Kcal/mol, respectively.

CONCLUSION

Coumarin rendered CRKP sensitive to meropenem as evidenced by its inhibitory action on hydrolytic activity and expression of carbapenemases. The current findings suggest that coumarin could be a possible solution to overcome carbapenems resistance in CRKP.

Qualitative and quantitative rapid detection of VOCs differentially released by VAP-associated bacteria using PTR-MS and FGC-PTR-MS

Ventilator-associated pneumonia (VAP) is a prevalent disease caused by microbial infection, resulting in significant morbidity and mortality within the intensive care unit (ICU). The rapid and accurate identification of pathogenic bacteria causing VAP can assist clinicians in formulating timely treatment plans. In this study, we attempted to differentiate bacterial species in VAP by utilizing the volatile organic compounds (VOCs) released by pathogens. We cultured 6 common bacteria in VAP in vitro, including Acinetobacter baumannii, Enterobacter cloacae, Escherichia coli, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Staphylococcus aureus, which covered most cases of VAP infection in clinic. After the VOCs released by bacteria were collected in sampling bags, they were quantitatively detected by a proton transfer reaction-mass spectrometry (PTR-MS), and the characteristic ions were qualitatively analyzed through a fast gas chromatography-proton transfer reaction-mass spectrometry (FGC-PTR-MS). After conducting principal component analysis (PCA) and analysis of similarities (ANOSIM), we discovered that the VOCs released by 6 bacteria exhibited differentiation following 3 h of quantitative cultivation in vitro. Additionally, we further investigated the variations in the types and concentrations of bacterial VOCs. The results showed that by utilizing the differences in types of VOCs, 6 bacteria could be classified into 5 sets, except for A. baumannii and E. cloacae which were indistinguishable. Furthermore, we observed significant variations in the concentration ratio of acetaldehyde and methyl mercaptan released by A. baumannii and E. cloacae. In conclusion, the VOCs released by bacteria could effectively differentiate the 6 pathogens commonly associated with VAP, which was expected to assist doctors in formulating treatment plans in time and improve the survival rate of patients.

On-site filtration of large sample volumes improves the detection of opportunistic pathogens in drinking water distribution systems

In this study, we compared conventional vacuum filtration of small volumes through disc membranes (effective sample volumes for potable water: 0.3-1.0 L) with filtration of high volumes using ultrafiltration (UF) modules (effective sample volumes for potable water: 10.6-84.5 L) for collecting bacterial biomass from raw, finished, and tap water at seven drinking water systems. Total bacteria, Legionella spp., Legionella pneumophila, Mycobacterium spp., and Mycobacterium avium complex in these samples were enumerated using both conventional quantitative PCR (qPCR) and viability qPCR (using propidium monoazide). In addition, PCR-amplified gene fragments were sequenced for microbial community analysis. The frequency of detection (FOD) of Legionella spp. in finished and tap water samples was much greater using UF modules (83% and 77%, respectively) than disc filters (24% and 33%, respectively). The FODs for Mycobacterium spp. in raw, finished, and tap water samples were also consistently greater using UF modules than disc filters. Furthermore, the number of observed operational taxonomic units and diversity index values for finished and tap water samples were often substantially greater when using UF modules as compared to disc filters. Conventional and viability qPCR yielded similar results, suggesting that membrane-compromised cells represented a minor fraction of total bacterial biomass. In conclusion, our research demonstrates that large-volume filtration using UF modules improved the detection of opportunistic pathogens at the low concentrations typically found in public drinking water systems and that the majority of bacteria in these systems appear to be viable in spite of disinfection with free chlorine and/or chloramine.IMPORTANCEOpportunistic pathogens, such as Legionella pneumophila, are a growing public health concern. In this study, we compared sample collection and enumeration methods on raw, finished, and tap water at seven water systems throughout the State of Minnesota, USA. The results showed that on-site filtration of large water volumes (i.e., 500-1,000 L) using ultrafiltration membrane modules improved the frequency of detection of relatively rare organisms, including opportunistic pathogens, compared to the common approach of filtering about 1 L using disc membranes. Furthermore, results from viability quantitative PCR (qPCR) with propidium monoazide were similar to conventional qPCR, suggesting that membrane-compromised cells represent an insignificant fraction of microorganisms. Results from these ultrafiltration membrane modules should lead to a better understanding of the microbial ecology of drinking water distribution systems and their potential to inoculate premise plumbing systems with opportunistic pathogens where conditions are more favorable for their growth.

Survival of a microbial inoculant in soil after recurrent inoculations

Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil-1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.

Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil

The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.

The Microbial Community Structure in the Rhizosphere of Theobroma cacao L. and Euterpe oleracea Mart. Is Influenced by Agriculture System in the Brazilian Amazon

This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices.

Culex pipiens and Culex restuans larval interactions shape the bacterial communities in container aquatic habitats

Container aquatic habitats host a community of aquatic insects, primarily mosquito larvae that browse on container surface microbial biofilm and filter-feed on microorganisms in the water column. We examined how the bacterial communities in these habitats respond to feeding by larvae of two container-dwelling mosquito species, Culex pipiens and Cx. restuans. We also investigated how the microbiota of these larvae is impacted by intra- and interspecific interactions. Microbial diversity and richness were significantly higher in water samples when mosquito larvae were present, and in Cx. restuans compared to Cx. pipiens larvae. Microbial communities of water samples clustered based on the presence or absence of mosquito larvae and were distinct from those of mosquito larvae. Culex pipiens and Cx. restuans larvae harbored distinct microbial communities when reared under intraspecific conditions and similar microbial communities when reared under interspecific conditions. These findings demonstrate that mosquito larvae play a major role in structuring the microbial communities in container habitats and that intra- and interspecific interactions in mosquito larvae may shape their microbiota. This has important ecological and public health implications since larvae of the two mosquito species are major occupants of container habitats while the adults are vectors of West Nile virus.